When this happens, you can tell that scanning is finished because there is no more screen activity, but QuarkXPress does not seem to want to close. This occurs randomly and is limited to QuarkXPress version 3.3.

The solution is to wait and leave Q++Studio and QuarkXPress alone.

QuarkXPress will close down gracefully after 2-3 minutes maximum. There has never been an occurrence of this "freeze false alert", where QuarkXPress did not eventually close down. The scanned template thus generated is fine and can be used as is.